def test_packmol_simulation_ternary():
smiles_list = ["Cc1ccccc1", "c1ccccc1", "CC"]
pdb_filenames = []
ligand_trajectories, ffxml = utils.smiles_to_mdtraj_ffxml(smiles_list)
for k, ligand_traj in enumerate(ligand_trajectories):
pdb_filename = tempfile.mktemp(suffix=".pdb")
ligand_traj.save(pdb_filename)
pdb_filenames.append(pdb_filename)
pdb_filenames = pdb_filenames[0:2] + [ligand_traj] # Test passing BOTH pdb filenames and trajectories as input.
trj = packmol.pack_box(pdb_filenames, [6, 11, 23])
xyz = trj.openmm_positions(0)
top = trj.top.to_openmm()
top.setUnitCellDimensions(mm.Vec3(*trj.unitcell_lengths[0])*u.nanometer)
forcefield = app.ForceField(ffxml)
temperature = 300 * u.kelvin
friction = 0.1 / u.picosecond
timestep = 0.1 * u.femtosecond
system = forcefield.createSystem(top, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * u.nanometers, constraints=None)
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
simulation = app.Simulation(top, system, integrator)
simulation.context.setPositions(xyz)
simulation.step(25)
def test_smiles_conversion():
pdb_filename = utils.get_data_filename("chemicals/proteins/1vii.pdb")
smiles = "Cc1ccccc1" # Also known as toluene.
temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 0.01 * u.femtosecond
protein_traj = md.load(pdb_filename)
protein_traj.center_coordinates()
protein_top = protein_traj.top.to_openmm()
protein_xyz = protein_traj.openmm_positions(0)
ligand_trajectories, ffxml = utils.smiles_to_mdtraj_ffxml([smiles])
ligand_traj = ligand_trajectories[0]
ligand_traj.center_coordinates()
eq(ligand_traj.n_atoms, 15)
eq(ligand_traj.n_frames, 1)
# Move the pre-centered ligand sufficiently far away from the protein to avoid a clash.
min_atom_pair_distance = (
((ligand_traj.xyz[0] ** 2.0).sum(1) ** 0.5).max() + ((protein_traj.xyz[0] ** 2.0).sum(1) ** 0.5).max() + 0.3
)
ligand_traj.xyz += np.array([1.0, 0.0, 0.0]) * min_atom_pair_distance
ligand_xyz = ligand_traj.openmm_positions(0)
ligand_top = ligand_traj.top.to_openmm()
forcefield = app.ForceField("amber10.xml", ffxml, "tip3p.xml")
model = app.modeller.Modeller(protein_top, protein_xyz)
model.add(ligand_top, ligand_xyz)
model.addSolvent(forcefield, padding=0.4 * u.nanometer)
system = forcefield.createSystem(
model.topology, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * u.nanometers, constraints=app.HAngles
)
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
simulation = app.Simulation(model.topology, system, integrator)
simulation.context.setPositions(model.positions)
print("running")
simulation.step(1)
def test_smiles_conversion():
pdb_filename = utils.get_data_filename("chemicals/proteins/1vii.pdb")
smiles = 'Cc1ccccc1' # Also known as toluene.
temperature = 300 * u.kelvin
friction = 0.3 / u.picosecond
timestep = 0.01 * u.femtosecond
protein_traj = md.load(pdb_filename)
protein_traj.center_coordinates()
protein_top = protein_traj.top.to_openmm()
protein_xyz = protein_traj.openmm_positions(0)
ligand_trajectories, ffxml = utils.smiles_to_mdtraj_ffxml([smiles])
ligand_traj = ligand_trajectories[0]
ligand_traj.center_coordinates()
eq(ligand_traj.n_atoms, 15)
eq(ligand_traj.n_frames, 1)
#Move the pre-centered ligand sufficiently far away from the protein to avoid a clash.
min_atom_pair_distance = ((ligand_traj.xyz[0]**2.).sum(1)**0.5).max() + (
(protein_traj.xyz[0]**2.).sum(1)**0.5).max() + 0.3
ligand_traj.xyz += np.array([1.0, 0.0, 0.0]) * min_atom_pair_distance
ligand_xyz = ligand_traj.openmm_positions(0)
ligand_top = ligand_traj.top.to_openmm()
forcefield = app.ForceField("amber10.xml", ffxml, "tip3p.xml")
model = app.modeller.Modeller(protein_top, protein_xyz)
model.add(ligand_top, ligand_xyz)
model.addSolvent(forcefield, padding=0.4 * u.nanometer)
system = forcefield.createSystem(model.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * u.nanometers,
constraints=app.HAngles)
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
simulation = app.Simulation(model.topology, system, integrator)
simulation.context.setPositions(model.positions)
print("running")
simulation.step(1)
def test_packmol_simulation_ternary_bydensity():
smiles_list = ["Cc1ccccc1", "c1ccccc1", "CC"]
pdb_filenames = []
ligand_trajectories, ffxml = utils.smiles_to_mdtraj_ffxml(smiles_list)
for k, ligand_traj in enumerate(ligand_trajectories):
pdb_filename = tempfile.mktemp(suffix=".pdb")
ligand_traj.save(pdb_filename)
pdb_filenames.append(pdb_filename)
pdb_filenames = pdb_filenames[0:2] + [
ligand_traj
] # Test passing BOTH pdb filenames and trajectories as input.
size = packmol.approximate_volume_by_density(smiles_list, [12, 22, 46])
trj = packmol.pack_box(pdb_filenames, [12, 22, 46], box_size=size)
# The box size should be set as expected (in nanometers).
assert all(
trj.unitcell_lengths[0] == [size / 10.0, size / 10.0, size / 10.0])
xyz = trj.openmm_positions(0)
top = trj.top.to_openmm()
top.setUnitCellDimensions(mm.Vec3(*trj.unitcell_lengths[0]) * u.nanometer)
forcefield = app.ForceField(ffxml)
temperature = 300 * u.kelvin
friction = 91.0 / u.picosecond
timestep = 0.1 * u.femtosecond
system = forcefield.createSystem(top,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * u.nanometers,
constraints=None)
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
simulation = app.Simulation(top, system, integrator)
simulation.context.setPositions(xyz)
simulation.minimizeEnergy()
simulation.step(25)
def test_packmol_simulation_ternary():
smiles_list = ["Cc1ccccc1", "c1ccccc1", "CC"]
pdb_filenames = []
ligand_trajectories, ffxml = utils.smiles_to_mdtraj_ffxml(smiles_list)
for k, ligand_traj in enumerate(ligand_trajectories):
pdb_filename = tempfile.mktemp(suffix=".pdb")
ligand_traj.save(pdb_filename)
pdb_filenames.append(pdb_filename)
pdb_filenames = pdb_filenames[0:2] + [
ligand_traj
] # Test passing BOTH pdb filenames and trajectories as input.
trj = packmol.pack_box(pdb_filenames, [6, 11, 23])
xyz = trj.openmm_positions(0)
top = trj.top.to_openmm()
top.setUnitCellDimensions(mm.Vec3(*trj.unitcell_lengths[0]) * u.nanometer)
forcefield = app.ForceField(ffxml)
temperature = 300 * u.kelvin
friction = 0.1 / u.picosecond
timestep = 0.1 * u.femtosecond
system = forcefield.createSystem(top,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * u.nanometers,
constraints=None)
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
simulation = app.Simulation(top, system, integrator)
simulation.context.setPositions(xyz)
simulation.step(25)
def test_packmol_simulation_ternary_bydensity():
smiles_list = ["Cc1ccccc1", "c1ccccc1", "CC"]
pdb_filenames = []
ligand_trajectories, ffxml = utils.smiles_to_mdtraj_ffxml(smiles_list)
for k, ligand_traj in enumerate(ligand_trajectories):
pdb_filename = tempfile.mktemp(suffix=".pdb")
ligand_traj.save(pdb_filename)
pdb_filenames.append(pdb_filename)
pdb_filenames = pdb_filenames[0:2] + [ligand_traj] # Test passing BOTH pdb filenames and trajectories as input.
size = packmol.approximate_volume_by_density( smiles_list, [12, 22, 46] )
trj = packmol.pack_box(pdb_filenames, [12, 22, 46], box_size = size)
# The box size should be set as expected (in nanometers).
assert all(trj.unitcell_lengths[0] == [size/10.0, size/10.0, size/10.0])
xyz = trj.openmm_positions(0)
top = trj.top.to_openmm()
top.setUnitCellDimensions(mm.Vec3(*trj.unitcell_lengths[0])*u.nanometer)
forcefield = app.ForceField(ffxml)
temperature = 300 * u.kelvin
friction = 91.0 / u.picosecond
timestep = 0.1 * u.femtosecond
system = forcefield.createSystem(top, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * u.nanometers, constraints=None)
integrator = mm.LangevinIntegrator(temperature, friction, timestep)
simulation = app.Simulation(top, system, integrator)
simulation.context.setPositions(xyz)
simulation.minimizeEnergy()
simulation.step(25)
